Question: Number of sequenced positions from a BAM file
0
gravatar for rubic
2.2 years ago by
rubic180
United States
rubic180 wrote:

Hi,

Is there a samtools or other tool command that given a bam (and/or indexed bam) file will report the number of sites sequenced?

rna-seq samtools bam • 541 views
ADD COMMENTlink modified 2.2 years ago by Devon Ryan90k • written 2.2 years ago by rubic180
0
gravatar for Devon Ryan
2.2 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

I'm sure there are a few out there (there's probably something in picard), but it's simple enough to pipe samtools depth through awk and just quickly count things. This has the benefit of allowing you to easily filter by MAPQ and other things.

ADD COMMENTlink written 2.2 years ago by Devon Ryan90k
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